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comparison msclust.xml @ 35:0ff22eec3e4b

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added peak_width_max for better performance
author pieter.lukasse@wur.nl
date Thu, 18 Sep 2014 14:29:57 +0200
parents 42880675f824
children 9018657a9f73
comparison
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34:e79a7c32b011 35:0ff22eec3e4b
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 ////////////////////////// 6 //////////////////////////
7 7
8 TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps 8 TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps
9 --> 9 -->
10 <command interpreter="java -jar -Xmx58g "> 10 <command interpreter="java -jar ">
11 MsClust.jar 11 MsClust.jar
12 -peaksFileName $inputPeaks 12 -peaksFileName $inputPeaks
13 -dataType $dataType 13 -dataType $dataType
14 -imputationMethod $imputationMethod.type 14 -imputationMethod $imputationMethod.type
15 #if $imputationMethod.type == "valueRange" 15 #if $imputationMethod.type == "valueRange"
26 -pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold 26 -pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold
27 -pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope 27 -pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
28 -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type 28 -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type
29 -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler 29 -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler
30 -rtDistanceConfidence $potDensFuncType.pdf_scan_conf 30 -rtDistanceConfidence $potDensFuncType.pdf_scan_conf
31 -peakWidthMax $potDensFuncType.rt_dist_tol_unit.peak_width_max
31 -centrotypesOut $centrotypesOut 32 -centrotypesOut $centrotypesOut
32 -simOut $simOut 33 -simOut $simOut
33 -micOut $micOut 34 -micOut $micOut
34 -mspOut $mspOut 35 -mspOut $mspOut
35 -classOut $classOut 36 -classOut $classOut
95 <option value="1" selected="true">scan nr</option> 96 <option value="1" selected="true">scan nr</option>
96 <option value="2" >(average) micro minutes</option> 97 <option value="2" >(average) micro minutes</option>
97 </param> 98 </param>
98 <when value="1"> 99 <when value="1">
99 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> 100 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
101 <param name="peak_width_max" type="float" size="10" value="30" label="MAX Peak Width, in scans" help="This parameter is to avoid calculations of correlation
102 between peaks that are too far apart anyway" />
100 </when> 103 </when>
101 <when value="2"> 104 <when value="2">
102 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" /> 105 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
106 <param name="peak_width_max" type="float" size="10" value="300000" label="MAX Peak Width, in micro minutes" help="This parameter is to avoid calculations of correlation
107 between peaks that are too far apart anyway" />
103 </when> 108 </when>
104 </conditional> 109 </conditional>
105 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> 110 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
106 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" /> 111 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
107 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> 112 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />